RetrogeneDB ID: retro_eeur_325

Retrocopy location

• Organism: Hedgehog (Erinaceus europaeus)
• Coordinates: scaffold_254725:3349..3619(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: None
• Aliases: None
• Status: NOVEL

Parental gene information

• Parental gene symbol: LLPH
• Ensembl ID: ENSEEUG00000012195
• Aliases: None
• Description: LLP homolog, long-term synaptic facilitation (Aplysia) [Source:HGNC Symbol;Acc:28229]

Sequence

>retro_eeur_325
TTAAAAAGCATTCTTAAAGTAGATACTGATGTTTTAATGAAAGATGTGCAAGAAACAGCAACTGTGGTGGCACCCAAACA
TTGTCAAGAGAAAAATCCAGTGTGTCATAGGAGATAAAAAGGTGACATGAAAATGGAGACTGAAATGAAGAGAAACACAA
AGAGCCTTCTAGACCGGCATGGACAATACCCCATATGGATGAACCAGAGACAAAGAAAAAGGCTGAAGGCAAAACAAGGG
AAATGGAAAGGCAAAAGTCAAAGCAAAAGC

Alignment

ORF - retro_eeur_325 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 80.43 %
• Parental protein coverage: 71.43 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  LKSILKVDTDVLMKDVQEIATVVAPKNCQEK-IQCEVEDEK-GDMKMETEIKRNKKSLLDQHGQYPIWMN
          LKSILKVDTDVLMKDVQE.ATVVAPK.CQEK.IQC...D.K.GDMKMETE.KRN.KSLLD.HGQYPIWMN
Retrocopy LKSILKVDTDVLMKDVQETATVVAPKHCQEK>IQCVIGDKK<GDMKMETEMKRNTKSLLDRHGQYPIWMN

Parental  QRQRKRLKAKREKRKGKSKANA
          QRQRKRLKAK..K.KGKS....
Retrocopy QRQRKRLKAKQGKWKGKSQSKS

Legend:

• *: Stop codon
• >: Forward frameshift by one nucleotide
• <: Reverse frameshift by one nucleotide

Expression

RNA-Seq

Expression validation based on RNA-Seq data:

Library	Retrocopy expression	Parental gene expression
SRP017611_brain	0.00 RPM	4.67 RPM
SRP017611_kidney	0.00 RPM	8.81 RPM
SRP017611_liver	0.00 RPM	4.50 RPM

ChIP-Seq

Erinaceus europaeus was not studied using ChIP-Seq data.

EST

Erinaceus europaeus was not studied using EST data.

TSS

Erinaceus europaeus was not studied using FANTOM5 data.

Lab

retro_eeur_325 was not experimentally validated.

Homology

Retrocopy orthology:

Erinaceus europaeus does not belong to any of the species groups (eutheria, teleost or neognath), studied for retrocopy-based homology. For more information about studied groups, please go to help section.

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Parental genes homology:

Parental genes homology involve 1 parental gene, and 1 retrocopy.

Species	Parental gene accession	Retrocopies number
Erinaceus europaeus	ENSEEUG00000012195	1 retrocopy	retro_eeur_325 ,